Intertidal seagrass beds are vital ecosystem engineers in estuarine environments, supporting highly productive macrobenthic communities. While excessive anthropogenic nutrient loads typically drive coastal eutrophication, recent evidence suggests that moderate wastewater discharges might act as a beneficial organic subsidy. This study evaluates the ecological quality of seagrass-associated macrobenthic communities near wastewater outfalls in the Tagus and Sado estuaries (central-western Portugal). We hypothesize that mild nutrient inputs enhance benthic abundance without compromising overall ecosystem health. Macrobenthic fauna, sediment properties, and physicochemical parameters were sampled during July 2021 and 2022 across 19 stations. Ecological quality was assessed using the AZTI Marine Biotic Index (AMBI) and multivariate AMBI (M-AMBI). Results demonstrate that seagrass meadows receiving moderate wastewater effluents exhibited higher macrofaunal abundance compared to unimpacted sites. This surge was not driven by opportunistic detritivores, but primarily by Peringia ulvae, a tolerant deposit-feeding gastropod. Although community structure displayed minor shifts toward tolerant taxa near outfalls, AMBI and M-AMBI scores classified most areas as maintaining 'Good' to 'High' Ecological Quality Status. Non-linear Generalized Additive Models (GAMs) confirmed a critical organic threshold (≃6% total organic matter), beyond which buffering capacity collapses into opportunist-dominated assemblages (Capitella capitata and Notomastus sp.). The dense seagrass canopy buffered organic enrichment, converting potential pollutants into a trophic subsidy rather than a driver of degradation. These findings advocate for habitat-specific reference baselines in marine monitoring frameworks to accurately distinguish beneficial subsidies from environmental degradation.